[R-sig-eco] interpreting adonis results

[yy.loh at york.ac.uk]

Hi all,

I've found the answer from some link.
http://permalink.gmane.org/gmane.comp.lang.r.ecology/1504

Cheers,
J 

On Nov 20 2011, yy.loh at york.ac.uk wrote:

>Thanks all for your help on adonis！！！^_^
>Thanks Kay too...;-)
>
>
>So,I have moved on and currently working on betadisper and faced some 
>problems.
>
>1.In vegatutor.pdf, betadisper (pg 33), "The function can only use one 
>factor as an independent variable, and it does not know the formula 
>interface,..."
> 
>mod <- with(dune.env, betadisper(betad, Management))
>
>Let's say I need to investigate the interaction of factors: Management and 
>USE. My question is: Can i create a new factor from the interaction of 
>factor Management and USE then use it in betadisper()? E.g.
>
>groupA<-interaction(dune.env$Management,dune.env$Use)
>mod <- with(dune.env, betadisper(betad, groupA))
>mod
>
>Error in optim(apply(X, 2, median, na.rm = TRUE), fn = medfun, gr = 
>dmedfun, :
>  non-finite value supplied by optim
>
>For the dune dataset, the above error occured. But for my data, the 
>interaction works. I wonder if i continue to use the new factor generated 
>from the factor-interaction for the betadisper, will it affects the 
>results? If this is wrong, what would be the recommended function to use?
>
>Sincerely Yours,
>J
>
>On Nov 17 2011, Kay Cecil Cichini wrote:
>
>>..to be save I would consider to exclude an effect due to different  
>>multivariate spread. See chapter 5.2, Homogeneity of groups and beta  
>>diversity, in the vegan tutorial at  
>>http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf.
>>
>>best,
>>kay
>>
>>
>>Zitat von Gavin Simpson <gavin.simpson at ucl.ac.uk>:
>>
>>> On Wed, 2011-11-16 at 03:43 +0100, Gian Maria Niccolò Benucci wrote:
>>>> Hi all,
>>>>
>>>> I had 84 samples collected in 7 different sites. In each sample were 
>>>> individuated the different fungal species and recorded. I would test 
>>>> if exist a real difference between the sites and if exist a sort of 
>>>> site effect that structure the fungal communities... Then, I did 
>>>> adonis test
>>>>
>>>> > adonis(community.sq ~ location, data=env.table, permutations=999)
>>>>
>>>> Call: adonis(formula = community.sq ~ location, data = env.table, 
>>>> permutations = 999)
>>>>
>>>>           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
>>>> location   6    12.593 2.09886  6.8867 0.34922  0.001 ***
>>>> Residuals 77    23.467 0.30477         0.65078
>>>> Total     83    36.060                 1.00000
>>>> ---
>>>> Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1
>>>>
>>>>
>>>>
>>>> The significance is R2=0.349 at P=0.001 Can I assure that exist a 
>>>> strong site effect in structuring the communities in each site?
>>>
>>> Depends. The test is one of no effect of `location`. You have found
>>> evidence against this hypothesis and thus could reject this hypothesis,
>>> instead accepting the alternative hypothesis that there is an effect of
>>> `location`. As to the strength of this effect? ~35% of the sums of
>>> squares can be explained by `location`. Substantially more of the
>>> variance remains unexplained. As I know nothing about your subject area,
>>> I am unable to comment further on the strength of the relationship.
>>>
>>> Seeing as many ecologists whose work I read would say an effect is
>>> significant if the p-value was >= 0.05. Not that I subscribe to this way
>>> or working, but by that criterion, you have identified a significant
>>> `location` effect.
>>>
>>> HTH
>>>
>>> G
>>>
>>>>
>>>> Thanks for helping,
>>>>
>>>> G.
>>>>
>>>> 	[[alternative HTML version deleted]]
>>>>
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>>>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>>>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
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>>
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>
>

-- 
Loh Yen Yee
Department of Biology (Area 18)
University of York
York, UK YO10 5DD